Okay, in retrospect, Tom did a great job at YSL. It was modern, sexy and oh so desirable.
YSL is such a mess today. Stefano's collections have been hit or miss, mostly misses. I hope Tom starts womenswear again.

So Tom join Gucci in 1990, and became creative director of that company in 1994.

He then became creative director for YSL in 1999 (?)

(This is where most of the confusion sets in) He then designed for both houses. Then he left YSL because of the difficulty he faced there. (What year I don't know, and also did the Gucci Group maintain ownership of YSL?)

However when he left YSL I don't think he was with Gucci, because everyone was so sad and there was a bit of uncertainty of what he would do next. So was he at Gucci the entire time he was with YSL, or did he eventually leave Gucci to focus on YSL, and then return to Gucci when that failed?

^^
tom left the Gucci Group in 2004. And apparently it was because of disagreements with owners (but I ignore if Pinault, who owns the group today, was the owner already, or if he had been during Ford's "reign")
Of course if he was out of the group, he couldn't design for Gucci nor Saint Laurent (which is indeed still part of the same group).
The "official" version says he left so he could focus on making movies, and the Yves-being-a-pain-in-the-*** thing, and all of that...
but again, new reasons surface from time to time.
He first said movies, then he has mentioned many times this "midlife crisis" he went through, then it was those Saint Laurent letters... i think the more successful he becomes with his later career, the more open he is to talking about it, so perhaps one day we will know all of the reasons

Ahhhh, you are so right how could I have forgotten about all that! Specially that YSL ad. But what I was talking is that his work is not as homoerotic as I wish it were, I want it on my face! Two male models making out naked on the beach wearing nothing but his sunglasses, that kind of homoerotic!

Do you know where I can find pictures or videos of that man on the stripper pole?

you must not have seen his article in out magazine (featured here) or the spring/summer 2008 look book (campaign?) with all of the naked male models (featured here).

as for video of his menswear finale show (fall/winter 2004-2005), it's hard to find much from that far back (the best i found came from new york magazine).

i'd still wear at least 80% of the pieces shown there. and between those gloriously soft looking coats, those damn awesome sunnies and that random guy dancing around the pole, what's there not to love?